[gmx-users] Gmx distance

Mon Nov 26 01:14:19 CET 2018

It will be calculating it based on the COM of the CNT, which will be a
single point, since that is what you are asking to do.

One way I can see is align the axis of the CNT so that it has the same
x,y coordinates all the way along, process in same manner, then
separate the distance in the x-y plan from your output data using
simple trigonometry.  Alternatively split box into slices along the
z-axis, so that the difference in the total distance at the top of the
slice versus middle of slice is sufficiently small (i.e. theta ~ 0),
calculate it for each slice, then average across all slices.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.

On Thu, 22 Nov 2018 at 23:35, rose rahmani <rose.rhmn93 at gmail.com> wrote:
>
> To be clear, i put 30 similar AA around NT i want to know how the average
> distance of group PROTEIN( consist of 30 AA ) varies during 100nS
> simulation. As i see in .gro file this distance decreased. I mean at the
> first moment i put them about 3nm far from Z axis of NT. THIS 3NM IS THE
> MINIMUM LENGTH OF A LINE BETWEEN AA COM POINT AND Z AXIS OF NT, AS YOU CAN
> IMAGINE THIS LINE IS PERPENDICULAR TO Z AXIS OF NT. this length is decrease
> after 100nS. But what i can't understand is that when i analyze it by
> g_dist( i select ZnS(NT) and Group Potein(=30 AA) in g_dist).. this is the
> result!
>
> Group     0 (         System) has 27831 elements
> Group     1 (          Other) has   408 elements
> Group     2 (            ZnS) has   408 elements
> Group     3 (        Protein) has   720 elements
> Group     4 (      Protein-H) has   390 elements
> Group     5 (        C-alpha) has    30 elements
> Group     6 (       Backbone) has    90 elements
> Group     7 (      MainChain) has    90 elements
> Group     8 (   MainChain+Cb) has   120 elements
> Group     9 (    MainChain+H) has   180 elements
> Group    10 (      SideChain) has   540 elements
> Group    11 (    SideChain-H) has   300 elements
> Group    12 (    Prot-Masses) has   720 elements
> Group    13 (    non-Protein) has 27111 elements
> Group    14 (          Water) has 26703 elements
> Group    15 (            SOL) has 26703 elements
> Group    16 (      non-Water) has  1128 elements
>
> Select a group: 2
> Selected 2: 'ZnS'
> Select a group: 3
> Selected 3: 'Protein'
>
>    0.0000000    0.2176011   -0.0120678   -0.0465498    0.2122209
>    1.0000000    0.2124534   -0.0301750   -0.0463870    0.2051198
>    2.0000000    0.1923753   -0.0158403   -0.0510135    0.1848106
>    3.0000000    0.1885315   -0.0107298   -0.0488160    0.1817856
>    4.0000000    0.2044982   -0.0052650   -0.0490329    0.1984630
>    5.0000000    0.2033602   -0.0002742   -0.0429537    0.1987720
>    6.0000000    0.2050487    0.0013833   -0.0444658    0.2001646
>    7.0000000    0.2002475    0.0041072   -0.0415003    0.1958568
>    8.0000000    0.2006473    0.0033450   -0.0511889    0.1939790
>    9.0000000    0.2032918   -0.0000119   -0.0330052    0.2005947
>   10.0000000    0.2255659    0.0003929   -0.0415857    0.2216990
>   11.0000000    0.2243811    0.0118313   -0.0344751    0.2214010
> .
> .
> .
> 99990.0000000    0.6195676   -0.1357532   -0.0029635    0.6045051
> 99991.0000000    0.5355353   -0.3716600    0.0125020    0.3853707
> 99992.0000000    0.5243484   -0.3698001    0.0180452    0.3712997
> 99993.0000000    0.4459361   -0.1407223   -0.2021322    0.3717511
> 99994.0000000    0.5592619   -0.3545561   -0.2162843    0.3745463
> 99995.0000000    0.5707593   -0.3472078   -0.2309759    0.3896961
> 99996.0000000    0.5238984   -0.3467841   -0.0103419    0.3925600
> 99997.0000000    0.5122938   -0.3379052    0.0097873    0.3849275
> 99998.0000000    0.5608831   -0.3396225   -0.2052171    0.3963993
> 99999.0000000    0.5230988   -0.3479364    0.0172603    0.3902240
> 100000.0000000    0.5158455   -0.3283865    0.0047119    0.3977897
>
> If the nanotube is along Z axis, so how g_dist calculate the COM of nano
> tube? Is it each point along Z axis which pass center of nano tube or COM
> in this case is just one point in the nanotube. If it is the second one, so
> g_dist doesn't calculate perpendicular distance from AA to Z axis... so it
> is completely different from what i want.
>
> How can i get what i want?
> this is exactly what want it is not an article it is just the figure 2
> https://www.sciencedirect.com/science/article/pii/S0008622314006691#f0010
>
>
> i'm completely confused!
> Please help me
>
> Best
> Rose
>
>
>
>
> On Wed, 7 Nov 2018, 18:32 Justin Lemkul <jalemkul at vt.edu wrote:
>
> >
> >
> > On 11/3/18 2:15 PM, rose rahmani wrote:
> > > On Sat, 3 Nov 2018, 19:56 Justin Lemkul <jalemkul at vt.edu wrote:
> > >
> > >>
> > >> On 11/2/18 11:36 AM, rose rahmani wrote:
> > >>> but this is output of -oall. its not a single value?!
> > >> You are asking in your command for all interatomic distances between the
> > >> groups (presumably, because you haven't shown your selection). This
> > >> command won't yield what you're hoping to see and my advice does not
> > >> apply for this type of situation (which doesn't seem to even match your
> > >> original statement of your problem).
> > >>
> > >>>     gmx distance -f md2.xtc -oall dist.xvg -n index.ndx
> > >>> # gmx distance is part of G R O M A C S:
> > >>> #
> > >>> #
> > >>>
> > >>
> > Â¸<8d><9a><9a><91>ÃÂ<9a><9b>ÃÂ°<8d><9e><91><98><9a>ÃÂ²<9e><98><9a><91><8b><9e>ÃÂ¾<85><8a><8d><9a>ÃÂ¼<86><9e><91>ÃÂ¬<94><86><9d><99a>8a><<
> > >>> #
> > >>> @    title "Distance"
> > >>> @    xaxis  label "Time (ps)"
> > >>> @    yaxis  label "Distance (nm)"
> > >>> @TYPE xy
> > >>>
> > >>>       1.000    0.229    0.229    0.446    0.582    0.446    0.229
> > 0.446
> > >>> 0.583    0.447    0.229    0.447    0.227    0.228    0.229    0.446
> > >>> 0.582    0.446    0.228    0.446    0.583    0.447    0.228    0.447
> > >>> 0.227    0.227    0.228    0.446    0.582    0.446    0.227    0.446
> > >>> 0.583    0.447    0.227    0.447    0.227    0.228    0.229    0.446
> > >>> 0.582    0.446    0.228    0.446    0.583    0.447    0.228    0.447
> > >>> 0.227    0.228    0.229    0.446    0.582    0.446    0.228    0.446
> > >>> 0.583    0.447    0.228    0.447    0.227    0.229    0.229    0.446
> > >>> 0.582    0.446    0.229    0.446    0.583    0.447    0.229    0.447
> > >>> 0.227    0.229    0.229    0.446    0.582    0.446    0.229    0.446
> > >>> 0.583    0.447    0.229    0.447    0.227    0.228    0.229    0.446
> > >>> 0.582    0.446    0.228    0.446    0.583    0.447    0.228    0.447
> > >>> 0.227    0.228    0.229    0.446    0.582    0.446    0.228    0.446
> > >>> 0.583    0.447    0.228    0.447    0.227    0.227    0.228    0.446
> > >>> 0.582    0.446    0.227    0.446    0.583    0.447    0.227    0.447
> > >>> 0.227    0.228    0.229    0.446    0.582    0.446    0.228    0.446
> > >>> 0.583    0.447    0.228    0.4
> > >>> .
> > >>> .
> > >>> .
> > >>>
> > >>> and this is -o of g_dist;
> > >>>    g_dist -f md2.xtc -s md2.tpr -n index -o all.xvg
> > >>> #
> > >>> # g_dist is part of G R O M A C S:
> > >>> #
> > >>> # GRowing Old MAkes el Chrono Sweat
> > >>> #
> > >>> @    title "Distance"
> > >>> @    xaxis  label "Time (ps)"
> > >>> @    yaxis  label "Distance (nm)"
> > >>> @TYPE xy
> > >>> @ view 0.15, 0.15, 0.75, 0.85
> > >>> @ legend on
> > >>> @ legend box on
> > >>> @ legend loctype view
> > >>> @ legend 0.78, 0.8
> > >>> @ legend length 2
> > >>> @ s0 legend "|d|"
> > >>> @ s1 legend "d\sx\N"
> > >>> @ s2 legend "d\sy\N"
> > >>> @ s3 legend "d\sz\N"
> > >>>      0.0000000    0.2176011   -0.0120678   -0.0465498    0.2122209
> > >>>      1.0000000    0.2124534   -0.0301750   -0.0463870    0.2051198
> > >>>      2.0000000    0.1923753   -0.0158403   -0.0510135    0.1848106
> > >>>      3.0000000    0.1885315   -0.0107298   -0.0488160    0.1817856
> > >>>      4.0000000    0.2044982   -0.0052650   -0.0490329    0.1984630
> > >>>      5.0000000    0.2033602   -0.0002742   -0.0429537    0.1987720
> > >>>      6.0000000    0.2050487    0.0013833   -0.0444658    0.2001646
> > >>>      7.0000000    0.2002475    0.0041072   -0.0415003    0.1958568
> > >>>      8.0000000    0.2006473    0.0033450   -0.0511889    0.1939790
> > >>>      9.0000000    0.2032918   -0.0000119   -0.0330052    0.2005947
> > >>>     10.0000000    0.2255659    0.0003929   -0.0415857    0.2216990
> > >>>     11.0000000    0.2243811    0.0118313   -0.0344751    0.2214010
> > >>>     12.0000000    0.2347855    0.0078275   -0.0383532    0.2314994
> > >>>     13.0000000    0.2371541    0.0081918   -0.0388267    0.2338107
> > >> Here, you have what you want (I assume), and the first column after the
> > >> time is all you need. It's the distance, which also can't be negative
> > >> because it is the magnitude of the vector length and is unsigned.
> > >>
> > > How S0 is calculated? Does it resulted from distance between COM of amino
> > > acid and COM of tube? Although, it is the magnitude of ... but it's
> >
> > The distance you get is the distance you ask for in your selection
> > (which isn't shown or stated). The distance formula is quite simple,
> > consult any geometry textbook.
> >
> > > calculated from x,y,z which may be negative and were not abaolute?! In
> > > addition, i put AAs (more than) 1.5 nm far from tube as an initial
> > > configuration, but any 1.5 nm distance..???
> > >
> >
> > A component of a vector may be positive or negative, these are just
> > differences along x, y, and z. The total length of a vector is a
> > magnitude and is therefore positive.
> >
> > -Justin
> >
> > >
> > >> -Justin
> > >>
> > >>> .
> > >>> .
> > >>> .
> > >>>
> > >>>
> > >>> On Thu, Nov 1, 2018 at 11:39 PM Justin Lemkul <jalemkul at vt.edu> wrote:
> > >>>
> > >>>> On 11/1/18 2:25 PM, rose rahmani wrote:
> > >>>>> I don't know how? I mean x,y,z(s1, s2,s3) in dist.xvg can easily be
> > >>>>> multiplied by (-), but how should i modify second column,i don't know
> > >> how
> > >>>>> s0 is calculated by g_distance to modify it??
> > >>>> The output of -oall is a single value, the actual distance, which I
> > >>>> assume is what you are talking about in your previous message. You can
> > >>>> parse that column in any scripting language you like and
> > >>>>
> > >>>> [ pseudocode, not functional ]
> > >>>> if (value < 0)
> > >>>> {
> > >>>>        value *= -1
> > >>>> }
> > >>>>
> > >>>> -Justin
> > >>>>> On Wed, 31 Oct 2018, 19:38 Justin Lemkul, <jalemkul at vt.edu> wrote:
> > >>>>>
> > >>>>>> On 10/31/18 12:06 PM, rose rahmani wrote:
> > >>>>>>> Hi,
> > >>>>>>>
> > >>>>>>> I want to calculate distances between fixed tube in the middle of
> > the
> > >>>> box
> > >>>>>>> and amino acids(all are same type)around it. But gmx distance gives
> > >> me
> > >>>>>> the
> > >>>>>>> relative distance i mean AA can be front or back( can be 0.5 or
> > -0.5
> > >>>> from
> > >>>>>>> tube) of  tube but still |-0.5|=0.5 nm far from it. How can i have
> > >> the
> > >>>>>>> absolute value of distances?
> > >>>>>>> Would you please help me?
> > >>>>>> Write a simple post-processing script that multiplies any negative
> > >> value
> > >>>>>> by -1.
> > >>>>>>
> > >>>>>> -Justin
> > >>>>>>
> > >>>>>> --
> > >>>>>> ==================================================
> > >>>>>>
> > >>>>>> Justin A. Lemkul, Ph.D.
> > >>>>>> Assistant Professor
> > >>>>>> Virginia Tech Department of Biochemistry
> > >>>>>>
> > >>>>>> 303 Engel Hall
> > >>>>>> 340 West Campus Dr.
> > >>>>>> Blacksburg, VA 24061
> > >>>>>>
> > >>>>>> jalemkul at vt.edu | (540) 231-3129
> > >>>>>> http://www.thelemkullab.com
> > >>>>>>
> > >>>>>> ==================================================
> > >>>>>>
> > >>>>>> --
> > >>>>>> Gromacs Users mailing list
> > >>>>>>
> > >>>>>> * Please search the archive at
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> > >>>>>>
> > >>>> --
> > >>>> ==================================================
> > >>>>
> > >>>> Justin A. Lemkul, Ph.D.
> > >>>> Assistant Professor
> > >>>> Virginia Tech Department of Biochemistry
> > >>>>
> > >>>> 303 Engel Hall
> > >>>> 340 West Campus Dr.
> > >>>> Blacksburg, VA 24061
> > >>>>
> > >>>> jalemkul at vt.edu | (540) 231-3129
> > >>>> http://www.thelemkullab.com
> > >>>>
> > >>>> ==================================================
> > >>>>
> > >>>> --
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> > >> --
> > >> ==================================================
> > >>
> > >> Justin A. Lemkul, Ph.D.
> > >> Assistant Professor
> > >> Virginia Tech Department of Biochemistry
> > >>
> > >> 303 Engel Hall
> > >> 340 West Campus Dr.
> > >> Blacksburg, VA 24061
> > >>
> > >> jalemkul at vt.edu | (540) 231-3129
> > >> http://www.thelemkullab.com
> > >>
> > >> ==================================================
> > >>
> > >> --
> > >> Gromacs Users mailing list
> > >>
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> > >> posting!
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> >
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Assistant Professor
> > Virginia Tech Department of Biochemistry
> >
> > 303 Engel Hall
> > 340 West Campus Dr.
> > Blacksburg, VA 24061
> >
> > jalemkul at vt.edu | (540) 231-3129
> > http://www.thelemkullab.com
> >
> > ==================================================
> >
> > --
> > Gromacs Users mailing list
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